The Gunners scored first through Tomas Rosicky before Giannis Maniatis and Kostas Mitroglou struck back for the Greek side in the second half to leave Wenger's men second in Group B behind German outfit Schalke.
Wenger admitted it was frustrating not to finish first in the group after his side led in Athens but was pleased with the contribution of his players, particularly the youngsters he handed playing time to as he rested a number of stars.
"It was an interesting game," he told ITV1.
"We had a good first half and we had two or three chances to score a second goal, but we needed a second goal tonight.
"The younger players did well for an hour, that is very positive. Now we have to wait for the draw, but ideally you want to finish first (in the group).
"The first goal was a goal kick, though, simple as that. What the referee behind the goal-line is doing nobody knows, but I don't think it was the right decision.
"We had a positive game. It was not the result we wanted but overall it was a very encouraging game."